12-76740371-C-G

Variant names:

• chr12-76740371-C-G
• rs10862477

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.324 in 152,058 control chromosomes in the GnomAD database, including 9,189 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (9189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49261 AN: 151940 Hom.: 9180 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.334

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49283 AN: 152058 Hom.: 9189 Cov.: 32 AF XY: 0.333 AC XY: 24766 AN XY: 74356

African (AFR) AF: 0.197 AC: 8173 AN: 41482

American (AMR) AF: 0.474 AC: 7240 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3466

East Asian (EAS) AF: 0.771 AC: 3988 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1523 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3949 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 21992 AN: 67962

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.319 Hom.: 1145

Bravo AF: 0.331

Asia WGS AF: 0.470 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10862477; hg19: chr12-77134151;